Right method to use for tiles of buildings in various phases of construction
I don't know which game engine you are using. But probably you could use 'shape keys'. At least in the bge that would work fine and it would be easy to set up. 

you crate different shape keys.

Than you create an animation with all the shape keys.

You can use logic Bricks to create a logic which controlls the animation with a property.

Than you just have to change the property and your building gets upgraded.
It also would be easy to crate a little blending animation so that the new stage doesn't just pop up.

Probably I didn't describe that too good so I added a .blend to Download where you can see what i mean. Just start the bge with p and use w and  s to transform the building.

I see that this method doesnt serve the job very well for a 2D java game.
Another method would be to use the 'restrict Rendering' Button in the Outliner.

The workflow would be:

Create the Building...



Than you mark everything which should be visible in the first stage. Go to frame 1 in the 'TimeLine' an Press i over the Camara Icon of ALL the Objects of the building.



Next you do the same for frame two...



The nice thing with this Method is that you now just can render an animation from Frame 1 to the Frame with the final stage (for example 5). If you configure your render output as in the picture below than you will get seperate Images of all Stages.



than you will get separate pictures of all stages.
I just pressed the animation button and had all the images int the right folder and with good names.



you also can configure the names by just writing the name behing the path.



Hopefully this is a good method for your project.